Loops were firstly called using the ABC Model. Since this method integrates ATAC-seq, H3K27ac and gene expression data when calling enhancer-promoter (E-P) pairs, we can be more confident we are truly calling loops. After defining E-P loops, differential loop calling was performed using a modified DESeq2 approach via Hictoolsr.

Differential loop analysis

Differential loop analysis was performed at 1000kb resolution (ie. regions were binned at 10kb windows).

Raw counts

Counts

E-P pairs

DESeq2 res

PCA

Top 500 most variable loops

All loops

MA plot